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Jacques Kallis stalled England's progress towards another dominant position in the third Test against South Africa, scoring an unbeaten hundred on the first day of the third Test to keep his side in the match at 279-6 at stumps.

Kallis shared half-century stands with AB de Villiers (36), Mark Boucher (51) and Dale Steyn (26 not out) to thwart England after two top-six batsmen made ducks. Kallis's efforts gave South Africa a more respectable close of play score than looked likely when they slumped to 127 for five in the afternoon session.

Kallis and Boucher's resolve was much needed after Graeme Swann extended his astonishing series with two wickets in two balls to take his winter tally to 16 so far.

England were perhaps sensing a short cut to further success, and the chance to move closer to a series victory after their win in Durban, but with their contrasting tempos Kallis and Boucher soon dented such hopes.

Their sixth-wicket partnership was threatening three figures when Stuart Broad finally got one to snake past Boucher's front-foot push and hit the back pad to win an lbw verdict that was not overturned on television referral.

Kallis found a new ally in Steyn, though, either side of the second new ball – which was taken under floodlights and almost brought the end for the No8, who escaped a tough chance at third slip where Jonathan Trott could not hold on off the bowling of James Anderson.

Kallis, meanwhile, was unhurried as he shut England out on his way to the 33rd Test century of his heavyweight career, and his third in succession against these opponents on this ground.

Tea

The sun has come out at Newlands this afternoon, just as England feared, but they have taken three wickets to win the session and put themselves in a strong position. And again it has been Graeme Swann who has played a key role in England's progress, with two wickets in as many balls.

England broke through without addition after lunch when, at 51, Graeme Smith pushed forward to James Anderson and got an outside edge to Prior.

The match – even the whole series, perhaps – was then in the balance. If Jacques Kallis and AB de Villiers were able to take their stand beyond tea – and this was a long, 150-minute session – England might be in big trouble.

The two doubled the score. But De Villiers looked fortunate when he had scored 24. England appeared to appeal for a catch behind and then had their umpire appeal turned down, but TV replays appeared to suggest that the batsman was out stumped. It did not matter very much.

Swann came into the match not in his first over, as we have come to expect, when he was brought into the attack at 83 for three, but in his eighth. South Africa appeared in the mood to play Swann more positively in this Test match and De Villiers, temperamentally as well as technically, was the batsman best equipped for the purpose.

But when he went down the wicket to the spinner he hit him straight to Andrew Strauss at short-midwicket. Then JP Duminy was out for a golden duck for the second time in as many innings, edging the spinner to the keeper; South Africa were 127 for five. Duminy's game appears to be in disarray.

Kallis, though, was holding the South Africa innings together once more and he moved to his fifty from 105 deliveries, with six fours in an over in which Swann was hit for three boundaries as South Africa part-recovered in the final half-hour of the session.

Lunch

South Africa, who were put in, had reached 51 for three just after lunch. England have bowled well generally, but it could have been much better for them.

Rain had delayed the start of play for half an hour and clouds swirled around Table Mountain and over Newlands. But as soon as England won the toss and chose to bowl – Andrew Strauss encouraged, perhaps, by the way the ball swung around during warm-up – you could almost feel the cloud cover being thrown off like a startled duvet at the alarm call.

As the morning went on the great mountain disrobed, coyly, and blue sky seemed to be rushing in from all directions, promising a more gentle afternoon for batting although immediately after lunch Jimmy Anderson had Graeme Smith well caught by a diving Matt Prior for 30.

England made a great start when, with only the fourth ball of the day, Anderson got one to lift and leave Ashwell Prince, a real pearler, and Prior took the catch.

But England should have had their second wicket with the first ball of the next over, bowled by Graham Onions. It was a little wide of off-stump and Smith, pushing at it, edged it straight to Graeme Swann at second slip. It was a straightforward waist-high catch but Swann grassed it.

"That will keep him quiet for a few minutes," said someone, for Swann is a cricketer who likes to chirrup and he has had much to chirrup about, man of the match in the first two Tests. Paul Collingwood normally fields there, but he is been grazing at mid-off, protecting his sore left index finger.

The miss looked worse then ever when Smith started to crunch a few. Onions made way for Stuart Broad with the score on 28 for one and immediately brought back a beauty which beat the inside of Smith's bat and was not far from clipping off stump.

One run later England had an appeal for a catch behind off Hashim Amla turned down and asked for a review, which also went against them. But England got Amla for 14, with the score on 46, shortly before lunch when Onions had him plumb lbw.